Assessment of the in situ biomethanation potential of a deep aquifer used for natural gas storage

The dihydrogen (H2) sector is undergoing development and will require massive storage solutions. To minimize costs, the conversion of underground geological storage sites, such as deep aquifers, used for natural gas storage into future underground hydrogen storage sites is the favored scenario. However, these sites contain microorganisms capable of consuming H2, mainly sulfate reducers and methanogens. Methanogenesis is, therefore expected but its intensity must be evaluated. Here, in a deep aquifer used for underground geological storage, 17 sites were sampled, with low sulfate concentrations ranging from 21.9 to 197.8 µM and a slow renewal of formation water. H2-selected communities mainly were composed of the families Methanobacteriaceae and Methanothermobacteriaceae and the genera Desulfovibrio, Thermodesulfovibrio, and Desulforamulus. Experiments were done under different conditions, and sulfate reduction, as well as methanogenesis, were demonstrated in the presence of a H2 or H2/CO2 (80/20) gas phase, with or without calcite/site rock. These metabolisms led to an increase in pH up to 10.2 under certain conditions (without CO2). The results suggest competition for CO2 between lithoautotrophs and carbonate mineral precipitation, which could limit microbial H2 consumption.

A deep continental aquifer downhole sampler for microbiological studies

To be effective, microbiological studies of deep aquifers must be free from surface microbial contaminants and from infrastructures allowing access to formation water (wellheads, well completions). Many microbiological studies are based on water samples obtained after rinsing a well without guaranteeing the absence of contaminants from the biofilm development in the pipes. The protocol described in this paper presents the adaptation, preparation, sterilization and deployment of a commercial downhole sampler (PDSshort, Leutert, Germany) for the microbiological studying of deep aquifers. The ATEX sampler (i.e., explosive atmospheres) can be deployed for geological gas storage (methane, hydrogen). To validate our procedure and confirm the need to use such a device, cell counting and bacterial taxonomic diversity based on high-throughput sequencing for different water samples taken at the wellhead or at depth using the downhole sampler were compared and discussed. The results show that even after extensive rinsing (7 bore volumes), the water collected at the wellhead was not free of microbial contaminants, as shown by beta-diversity analysis. The downhole sampler procedure was the only way to ensure the purity of the formation water samples from the microbiological point of view. In addition, the downhole sampler allowed the formation water and the autochthonous microbial community to be maintained at in situ pressure for laboratory analysis. The prevention of the contamination of the sample and the preservation of its representativeness are key to guaranteeing the best interpretations and understanding of the functioning of the deep biosphere.

Biological, geological and chemical effects of oxygen injection in underground gas storage aquifers in the setting of biomethane deployment

The last few years have seen the proliferation of anaerobic digestion plants to produce biomethane. Oxygen (O₂) traces added to biogas during the desulfurization process are co-injected in the gas network and can be stored in Underground Gas Storage (UGS). However, there are no data available for the undesirable effects of O₂ on these anoxic environments, especially on deep aquifers. In addition to mineral alteration, O₂ can have an impact on the anaerobic autochthonous microbial life. In our study, the storage conditions of an UGS aquifer were reproduced in a high-pressure reactor and bio-geo-chemical interactions between the aqueous, gas and solid phases were studied. Sulfate was depleted from the liquid phase for three consecutive times during the first 130 days of incubation reproducing the storage conditions (36 °C, 60 bar, methane with 1% CO₂). Sulfate-reducers, such as Desulfovibrionaceae, were identified from the high-pressure system. Simulations with PHREEQC were used to determine the thermodynamic equilibrium to confirm any gas consumption. CO₂ quantities decreased in the gas phase, suggesting its use as carbon source by microbial life. Benzene and toluene, hydrocarbons found in traces and known to be biodegradable in storages, were monitored and a decrease of toluene was revealed and associated to the Peptococcaceae family. Afterwards, O₂ was added as 1% of the gas phase, corresponding to the maximum quantity found in biomethane after desulfurization process. Re-oxidation of sulfide to sulfate was observed along with the end of sulfate reducing activity and toluene biodegradation and the disappearance of most of the community. H₂ surprisingly appeared and accumulated as soon as hydrogenotrophic sulfate-reducers decreased. H₂ would be produced via the necromass fermentation accomplished by microorganisms able to resist the oxic conditions of 4.42·10^-4 mol.Kgw^-1 of O₂. The solid phase composed essentially of quartz, presented no remarkable changes.

Microbial Diversity Under the Influence of Natural Gas Storage in a Deep Aquifer

Deep aquifers (up to 2km deep) contain massive volumes of water harboring large and diverse microbial communities at high pressure. Aquifers are home to microbial ecosystems that participate in physicochemical balances. These microorganisms can positively or negatively interfere with subsurface (i) energy storage (CH4 and H2), (ii) CO2 sequestration; and (iii) resource (water, rare metals) exploitation. The aquifer studied here (720m deep, 37°C, 88bar) is naturally oligotrophic, with a total organic carbon content of <1mg.L-1 and a phosphate content of 0.02mg.L-1. The influence of natural gas storage locally generates different pressures and formation water displacements, but it also releases organic molecules such as monoaromatic hydrocarbons at the gas/water interface. The hydrocarbon biodegradation ability of the indigenous microbial community was evaluated in this work. The in situ microbial community was dominated by sulfate-reducing (e.g., Sva0485 lineage, Thermodesulfovibriona, Desulfotomaculum, Desulfomonile, and Desulfovibrio), fermentative (e.g., Peptococcaceae SCADC1_2_3, Anaerolineae lineage and Pelotomaculum), and homoacetogenic bacteria ("Candidatus Acetothermia") with a few archaeal representatives (e.g., Methanomassiliicoccaceae, Methanobacteriaceae, and members of the Bathyarcheia class), suggesting a role of H2 in microenvironment functioning. Monoaromatic hydrocarbon biodegradation is carried out by sulfate reducers and favored by concentrated biomass and slightly acidic conditions, which suggests that biodegradation should preferably occur in biofilms present on the surfaces of aquifer rock, rather than by planktonic bacteria. A simplified bacterial community, which was able to degrade monoaromatic hydrocarbons at atmospheric pressure over several months, was selected for incubation experiments at in situ pressure (i.e., 90bar). These showed that the abundance of various bacterial genera was altered, while taxonomic diversity was mostly unchanged. The candidate phylum Acetothermia was characteristic of the community incubated at 90bar. This work suggests that even if pressures on the order of 90bar do not seem to select for obligate piezophilic organisms, modifications of the thermodynamic equilibria could favor different microbial assemblages from those observed at atmospheric pressure.

Genome insights of mercury methylation among Desulfovibrio and Pseudodesulfovibrio strains

Mercury methylation converts inorganic mercury into the toxic methylmercury, and the consequences of this transformation are worrisome for human health and the environment. This process is performed by anaerobic microorganisms, such as several strains related to Pseudodesulfovibrio and Desulfovibrio genera. In order to provide new insights into the molecular mechanisms of mercury methylation, we performed a comparative genomic analysis on mercury methylators and non-methylators from (Pseudo)Desulfovibrio strains. Our results showed that (Pseudo)Desulfovibrio species are phylogenetically and metabolically distant and consequently, these genera should be divided into various genera. Strains able to perform methylation are affiliated with one branch of the phylogenetic tree, but, except for hgcA and hgcB genes, no other specific genetic markers were found among methylating strains. hgcA and hgcB genes can be found adjacent or separated, but proximity between those genes does not promote higher mercury methylation. In addition, close examination of the non-methylator Pseudodesulfovibrio piezophilus C1TLV30 strain, showed a syntenic structure that suggests a recombination event and may have led to hgcB depletion. The genomic analyses identify also arsR gene coding for a putative regulator upstream hgcA. Both genes are cotranscribed suggesting a role of ArsR in hgcA expression and probably a role in mercury methylation.

Geological gas-storage shapes deep life

Around the world, several dozen deep sedimentary aquifers are being used for storage of natural gas. Ad hoc studies of the microbial ecology of some of them have suggested that sulfate reducing and methanogenic microorganisms play a key role in how these aquifers' communities function. Here, we investigate the influence of gas storage on these two metabolic groups by using high-throughput sequencing and show the importance of sulfate-reducing Desulfotomaculum and a new monophyletic methanogenic group. Aquifer microbial diversity was significantly related to the geological level. The distance to the stored natural gas affects the ratio of sulfate-reducing Firmicutes to deltaproteobacteria. In only one aquifer, the methanogenic archaea dominate the sulfate-reducers. This aquifer was used to store town gas (containing at least 50% H₂ ) around 50 years ago. The observed decrease of sulfates in this aquifer could be related to stimulation of subsurface sulfate-reducers. These results suggest that the composition of the microbial communities is impacted by decades old transient gas storage activity. The tremendous stability of these gas-impacted deep subsurface microbial ecosystems suggests that in situ biotic methanation projects in geological reservoirs may be sustainable over time.

Pseudodesulfovibrio hydrargyri sp. nov., a mercury-methylating bacterium isolated from a brackish sediment

The strain BerOc1^T was isolated from brackish sediments contaminated with hydrocarbons and heavy metals. This strain has been used as a model strain of sulfate-reducer to study the biomethylation of mercury. The cells are vibrio-shaped, motile and not sporulated. Phylogeny and physiological traits placed this strain within the genus Pseudodesulfovibrio. Optimal growth was obtained at 30 °C, 1.5 % NaCl and pH 6.0-7.4. The estimated G+C content of the genomic DNA was 62.6 mol%. BerOc1^T used lactate, pyruvate, fumarate, ethanol and hydrogen. Terminal electron acceptors used were sulfate, sulfite, thiosulfate and DMSO. Only pyruvate could be used without a terminal electron acceptor. The major fatty acids were C18 : 0, anteiso-C15 : 0, C16 : 0 and C18 : 1ω7. The name Pseudodesulfovibrio hydrargyri sp. nov. is proposed for the type strain BerOc1^T (DSM 10384^T=JCM 31820^T).

Desulfotomaculum aquiferis sp. nov. and Desulfotomaculum profundi sp. nov., isolated from a deep natural gas storage aquifer

Two novel strictly anaerobic bacteria, strains Bs105T and Bs107T, were isolated from a deep aquifer-derived hydrocarbonoclastic community. The cells were rod-shaped, not motile and had terminal spores. Phylogenetic affiliation and physiological properties revealed that these isolates belong to two novel species of the genus Desulfotomaculum. Optimal growth temperatures for strains Bs105T and Bs107T were 42 and 45 °C, respectively. The estimated G+C content of the genomic DNA was 42.9 and 48.7 mol%. For both strains, the major cellular fatty acid was palmitate (C16 : 0). Specific carbon fatty acid signatures of Gram-positive bacteria (iso-C17 : 0) and sulfate-reducing bacteria (C17 : 0cyc) were also detected. An insertion was revealed in one of the two 16S rRNA gene copies harboured by strain Bs107T. Similar insertions have previously been highlighted among moderately thermophilic species of the genus Desulfotomaculum. Both strains shared the ability to oxidize aromatic acids (Bs105T: hydroquinone, acetophenone, para-toluic acid, 2-phenylethanol, trans-cinnamic acid, 4-hydroxybenzaldehyde, benzyl alcohol, benzoic acid 4-hydroxybutyl ester; Bs107T: ortho-toluic acid, benzoic acid 4-hydroxybutyl ester). The names Desulfotomaculum aquiferis sp. nov. and Desulfotomaculum profundi sp. nov. are proposed for the type strains Bs105T (=DSM 24088T=JCM 31386T) and Bs107T (=DSM 24093T=JCM 31387T).

Mercury methylation by a microbial community from sediments of the Adour Estuary (Bay of Biscay, France)

In order to study the influence of microorganisms on the mercury biogeochemistry, the metal content and the structure of microbial communities were determined in sediments from stations along the Adour Estuary. The comparison of the bacterial communities and their distribution in function of the environmental parameters by Canonical Correspondence Analysis (CCA) revealed the influence of metals on the bacterial communities structure. Sediments where the bacterial communities are mostly influenced by methylmercury were incubated in slurries with or without mercury, under oxic and anoxic conditions. Methylmercury production was detected in the anoxic biotic slurries with a net methylation yield of 0.3% after 24 h. CCA based on T-RFLP profiles revealed the impact of mercury addition on the bacterial communities structure. In addition, 17 bacterial strains, mainly sulphate-reducing bacteria involved in mercury methylation, were isolated and identified.